As far as I know, when you are creating new Application in SCCM it starts as 64bit process by default. You can set an option to 'start as 32 bit process on 64bit OS' as you can see at the bottom of this image:
http://myitforum.com/myitforumwp/2012/06/26/configmgr-2012-console-automated-deployment-walkthrough/6-26-2012-2-12-11-pm/

This doesn't apply for the 'Package' model so when you are using SCCM packages you should consider mentioned above 'sysnative' command.